This work presents results from the selective microstructuring of a master for an injection molding die using ultrashort laser pulses. Possible applications for such methods in the production of microfluidic and biochips are found in the fields of rapid prototyping and mastering. As an example structure, a microfluidic chip is processed, which is intended for applications in life sciences and diagnostics. This is a bio-inspired microsystem that simulates the interface between alveoli and capillaries in the human lung. Due to the short pulse durations in the femtosecond range, material can be 'cold' processed because of minimal thermal diffusion, while highly bandgap materials absorb laser radiation at wavelengths for which they would normally be transparent through nonlinear processes. Furthermore, this work presents previous results of selective structuring using a femtosecond laser on photoresist in combination with conventional UV photolithography. By combining these two methods, a structure can be created that contains both micro and millimeter structures.